## renaming the first element in assays to 'counts'## converting counts to integer mode## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 1994 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing## [1] "Intercept" "paper_IDH.status_WT_vs_Mutant"res <- results(ddsSE, name = "paper_IDH.status_WT_vs_Mutant")
dea <- as.data.frame(res)
summary(res)##
## out of 46068 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 3336, 7.2%
## LFC < 0 (down) : 2742, 6%
## outliers [1] : 0, 0%
## low counts [2] : 12505, 27%
## (mean count < 1)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.1 (2019-07-05)
## os Ubuntu 19.10
## system x86_64, linux-gnu
## ui X11
## language en_US
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2019-12-02
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## ! package * version date lib source
## acepack 1.4.1 2016-10-29 [2] CRAN (R 3.6.1)
## annotate 1.64.0 2019-10-29 [1] Bioconductor
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## Biostrings 2.54.0 2019-10-29 [1] Bioconductor
## bit 1.1-14 2018-05-29 [2] CRAN (R 3.6.1)
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## downloader 0.4 2015-07-09 [2] CRAN (R 3.6.1)
## dplyr 0.8.3 2019-07-04 [2] CRAN (R 3.6.1)
## EDASeq 2.20.0 2019-10-29 [1] Bioconductor
## edgeR 3.28.0 2019-10-29 [1] Bioconductor
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##
## [1] /home/tiagochst/R/x86_64-pc-linux-gnu-library/3.6
## [2] /usr/local/lib/R/site-library
## [3] /usr/lib/R/site-library
## [4] /usr/lib/R/library
##
## R ── Package was removed from disk.